fp-bio-2 biochemistry 2

7/29/2019 FP-Bio-2 biochemistry 2

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Proteins are the most abundant and functionally divers

molecules in living systems. Every life process depends onthis class of molecules.

Amino Acids and Proteins

1. Enzymes - increase rate of reaction x 1 billion2. Carriers hemoglobin, transferrin

3. Receptors hormones, cytokines

4. Transport membrane channels

5. Structure collagen, elastin

6. Protective - immunoglobulins

7. Contractile - muscle, cytoskeleton

8. Regulatory (Hormones) govern metabolic pathway

Types and functions of Proteins


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Structure of Proteins

-The linear sequence of amino acids contain the necessary information to

generate protein molecule with a unique three-dimensional structure. Theprotein structure is describe by the following structural levels of

Primary

Secondary

Tertiary

Quaternary

Primary Structure of Proteins

-The amino acids sequence of in protein. Amino acids are covalently joined bypeptide bonds between -carboxyl group of one amino acid and -amino group

with other amino acid.

- many genetic disease results from abnormal amino acid sequence.

-There are different techniques for protein sequencing.


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4 Levels of Protein Structure


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The Peptide Bond

Amide bond formed by the COOH of an amino acid and the NH2 of the next amino acid

peptide bond


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Secondary Structure of Proteins-The polypeptide backbone dose not assume a random

three-dimensional structure but forms regular

arrangements of amino acids that located near to each

other in linear sequence called Secondary Structure

-helix

-Sheet

-turns

Weak Noncovalent Interactions

-helix:- It is spiral structure, consisting of tightly packed,

coiled polypeptide backbone core

-The amino acid side chains are extending outward from

central axis avoid interfering steriecally with each

other.- a very divers group of proteins contains -helix;

Keratins and fibrous proteins

- Stabilized by hydrogen bonding between peptide bond

Oxygen and amide hydrogen. H-bonds individually are

weak by collectively can stabilize the helix.


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*Some amino acids disrupt the -helix eg.

Proline: bec of its imino group is not

geometrically compatible with spiral structure of

-helix , its inserts a Kink in the chain.

Large no. of charged amino acids (glutamate,aspartate, histideine, lysine arginine) forming

ionic bonds or electrostatic repulsion

amino acids with bulky side chains (tryptophan)

amino acids with branched side chain like Valine

and isolucine.


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-Sheet:-Another form of the secondary structure in which all of the

peptide bond components are involved in H-bonding

- The surface of -Sheet appear pleated called -pleated

sheet

- The backbone of polypeptide chain is extended into Zigzag

rather than helical structure

- are usually represented by broad arrows

- are composed of two or more peptide chains (-strands) or

segments of polypeptide chains that are fully extended.

- The hydrogen bonds are perpendicular to the polypeptide

backbone.


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Tertiary structure- The structure of globular protein in aqueous solution is compact

-Hydrophobic side chains are buried in the interior while hydrophilic groups are

generally found on the surface- Hydrophilic a.a and peptide bond component that found in the interior of the

protein are occupied by H-bonding so cannot form H-bonds with water


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Interaction stabilizing the tertiary structure-Amino acid sequence determines the unique three-dimensional

structure of each polypeptide

- Interactions between amino acid side chains guide the folding

pathway of a polypeptide into a compact structure.

-The cooperation of four types of interactions stabilizes the tertiary

structure of a protein

1-Disulfide bonds:

Two cysteine resides are oxidized into cystine with S-S linkage

The folding of polypeptide can bring the cysteine residues in

proximity and permit covalent bonding

the disulfide bond is covalent and strong bond and stabilizes the

proteins


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2-Hydrophobic interaction: Amino acids with non-polar side chain located in the interior of

the polypeptide molecule and can associate with other hydrophobic

amino acids. Amino acids with polar or charged side chains tend to be located on

the surface of the molecule.

3-Hydrogen interaction:Amino acid side chain containing oxygen or nitrogen-bound hydrogen asserine, or threonine can form H-bonds with electron rich atoms as

carbonyl oxygen of the peptide bonds.

4-Ionic interaction:Negatively charged group in the side chain of aspartate or glutamate

can interact with positively charged groups as the amino group(-NH3)

in the side chain of lysine


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Quaternary Structure of Proteins:

-Monomeric proteins: consist of a single polypeptide chain.

Other proteins consist of two or more polypeptide chains that maybe structurally identical or totally unrelated.

two subunit protein is called dimeric protein, three subunit is called

trimeric . Multimeric protein has several subunit

The arrangement of these subunit is called Quaternary structure Subunits are associated together by non-covalent interactions

(hydrophobic, hydrogen interactions) or covalent interactions like

disulfide linkage

Subunit may either function independently or may workcooperatively


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The Four Levels of Protein Structure


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Protein Classification

Simple composed only of amino acid residues

Conjugated contain prosthetic groups

(metal ions, co-factors, lipids, carbohydrates)

Example: Hemoglobin Heme


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Protein Classification

One polypeptide chain - monomeric protein More than one - multimeric protein

Homomultimer - one kind of chain

Heteromultimer - two or more differentchains

(e.g. Hemoglobin is a heterotetramer. It hastwo alpha chains and two beta chains.)


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Protein ClassificationFibrous1) polypeptides arranged in long strands or

sheets2) water insoluble (lots of hydrophobic AAs)3) strong but flexible

4) Structural (keratin, collagen)

Globular

1) polypeptide chains folded into spherical orglobular form2) water soluble3) contain several types of secondary structure4) diverse functions (enzymes, regulatory

proteins)


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Protein Function

Catalysis enzymes

Structural keratin

Transport hemoglobin

Trans-membrane transport Na+/K+ ATPases Toxins rattle snake venom, ricin

Contractile function actin, myosin

Hormones insulin

Storage Proteins seeds and eggs Defensive proteins antibodies

fp-bio-2 biochemistry 2

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